Molecular methods for the detection and classification of Cryptosporidium

Cryptosporidiosis is a zoonotic disease caused by a parasitic protozoan belonging to the coccidial genus Cryptosporidium. Current laboratory methods are adequate for the detection of the infection when oocysts are present in great numbers, but more-sensitive means of identification are urgently required. In a recent issue of Parasitology Today, Carolyn Petersen has presented a review of the cell biology of this parasite'. Here, Kath Webster draws attention to the various methods involved in its detection and classification.     

Obtaining Reliable Likelihood Ratio Tests from Simulated Likelihood Functions

Mixed models

Models allowing for continuous heterogeneity by assuming that value of one or more parameters follow a specified distribution have become increasingly popular. This is known as ‘mixing’ parameters, and it is standard practice by researchers - and the default option in many statistical programs - to base test statistics for mixed models on simulations using asymmetric draws (e.g. Halton draws).

Problem 1: Inconsistent LR tests due to asymmetric draws:

This paper shows that when the estimated likelihood functions depend on standard deviations of mixed parameters this practice is very likely to cause misleading test results for the number of draws usually used today. The paper illustrates that increasing the number of draws is a very inefficient solution strategy requiring very large numbers of draws to ensure against misleading test statistics. The main conclusion of this paper is that the problem can be solved completely by using fully antithetic draws, and that using one dimensionally antithetic draws is not enough to solve the problem.

Problem 2: Maintaining the correct dimensions when reducing the mixing distribution:

A second point of the paper is that even when fully antithetic draws are used, models reducing the dimension of the mixing distribution must replicate the relevant dimensions of the quasi-random draws in the simulation of the restricted likelihood. Again this is not standard in research or statistical programs. The paper therefore recommends using fully antithetic draws replicating the relevant dimensions of the quasi-random draws in the simulation of the restricted likelihood and that this should become the default option in statistical programs. JEL classification: C15; C25.     

Visual exploration across biomedical databases

Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration. A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases. Databases are modeled as an entity-relation graph containing nodes (database records) and links (relationships between records). Users specify a keyword search string to retrieve an initial set of nodes, and then explore intra- and interdatabase links. Results are visualized with user-defined semantic substrates to take advantage of the rich set of attributes usually present in biomedical data. Comments from domain experts indicate that this visualization method is potentially advantageous for biomedical knowledge exploration.     

When ancient meets modern: the relationship between postpartum non-susceptibility and contraception in sub-Saharan Africa

Extended durations of postpartum non-susceptibility (PPNS) comprising lactational amenorrhoea and associated taboos on sex have been a central component of traditional reproductive regimes in sub-Saharan Africa. In situations of rising contraceptive prevalence this paper draws on data from the Demographic Health Surveys to consider the neglected interface between ancient and modern methods of regulation. The analysis reports striking contrasts between countries. At one extreme a woman's natural susceptibility status appears to have little bearing on the decision to use contraception in Zimbabwe, with widespread 'double-protection'. By contrast, contraceptive use in Kenya and Ghana builds directly onto underlying patterns of PPNS. Possible explanations for the differences and the implications for theory and policy are discussed.     

Characterization of soil samples by enzyme activity

The presence of extracellular enzymes in soils offers a very sensitive method for matching, or distinguishing between, soil samples. Simple colorimetric methods were used to compare enzyme levels in soils from different sites. It was found that each soil tested had its own spectrum of enzyme activity, by which it could be characterized and thereby distinguished from other soils that were essentially similar in physical composition.

This article describes nine simple enzyme assays used by sixth-form students for ‘soilprinting’, and draws attention to some possible applications of the technique in forensic science and in studies of soil fertility.     

长春市人口综合调控对策研究

正确预测和掌握人口的发展规律对于合理制定人口政策、控制人口增长、保持社会稳定都具有十分重要的意义。应用系统动力学的原理和方法,对长春市的人口进行了动态仿真研究,认为长春市的人口增长以机械增长为主。综合考虑了人口的出生率、死亡率、人口政策、环境污染、经济发展水平、育龄妇女生育指数等对人口有重要影响的几个因子。对人口系统的预测应重点放在控制额定迁入率、转变经济增长方式、提高用人效率和调整劳动力结构等方面的人口调控对策。     

TREECON: A software package for the construction and drawing of evolutionary trees

A package of programs (run by a management program called TREECON)was developed for the construction and drawing of evolutionarytrees. The program MATRIX calculates dissimilarity values andcan perform bootstrap analysis on nucleic acid sequences. TREEimplements different evolutionary tree constructing methodsbased on distance matrices. Because some of these methods produceunrooted evolutionary trees, a program ROOT places a root onthe tree. Finally, the program DRAW draws the evolutionary tree,changes its size or topology, and produces drawings suitablefor publication. Whereas MATRIX is suited only for nucleic acids,the modules TREE, ROOT and DRAW are applicable to any kind ofdissimilarity matrix. The programs run on IBM-compatible microcomputersusing the DOS operating system.     

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae)

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.     

Mathematical simulation of forced expiration

Flow limitation during forced expiration is simulated by a mathematical model. This model draws on the pressure-area law obtained in the accompanying paper, and the methods of analysis for one-dimensional flow in collapsible tubes developed by Shapiro (Trans. ASME J. Biomech. Eng. 99: 126-147, 1977). These methods represent an improvement over previous models in that 1) the effects of changing lung volume and of parenchymal-bronchial interdependence are simulated; 2) a more realistic representation of collapsed airways is employed; 3) a solution is obtained mouthward of the flow-limiting site by allowing for a smooth transition from sub- to supercritical flow speeds, then matching mouth pressure by imposing an elastic jump (an abrupt transition from super- to subcritical flow speeds) at the appropriate location; and 4) the effects of levels of effort (or vacuum pressure) in excess of those required to produce incipient flow limitation are examined, including the effects of potential physiological limitation.     

On statistical methods for comparison of intrasample morphometric variability: Zalavár revisited

In studies of morphology, methods for comparing amounts of variability are often important. Three different ways of utilizing determinants of covariance matrices for testing for surplus variability in a hypothesis sample compared to a reference sample are presented: an F-test based on standardized generalized variances, a parametric bootstrap based on draws on Wishart matrices, and a nonparametric bootstrap. The F-test based on standardized generalized variances and the Wishart-based bootstrap are applicable when multivariate normality can be assumed. These methods can be applied with only summary data available. However, the nonparametric bootstrap can be applied with multivariate nonnormally distributed data as well as multivariate normally distributed data, and small sample sizes. Therefore, this method is preferable when raw data are available. Three craniometric samples are used to present the methods. A Hungarian Zalavár sample and an Austrian Berg sample are compared to a Norwegian Oslo sample, the latter employed as reference sample. In agreement with a previous study, it is shown that the Zalavár sample does not represent surplus variability, whereas the Berg sample does represent such a surplus variability.     

The separation of timescales in Bayesian survival modeling of the time-varying effect of a time-dependent exposure

In this paper, we apply flexible Bayesian survival analysis methods to investigate the risk of lymphoma associated with kidney transplantation among patients with end-stage renal disease. Of key interest is the potentially time-varying effect of a time-dependent exposure: transplant status. Bayesian modeling of the baseline hazard and the effect of transplant requires consideration of 2 timescales: time since study start and time since transplantation, respectively. Previous related work has not dealt with the separation of multiple timescales. Using a hierarchical model for the hazard function, both timescales are incorporated via conditionally independent stochastic processes; smoothing of each process is specified via intrinsic conditional Gaussian autoregressions. Features of the corresponding posterior distribution are evaluated from draws obtained via a Metropolis-Hastings-Green algorithm.     

Aggregation of measures to produce an overall assessment of animal welfare. Part 1: a review of existing methods

Several systems have been proposed for the overall assessment of animal welfare at the farm level for the purpose of advising farmers or assisting public decision-making. They are generally based on several measures compounded into a single evaluation, using different rules to assemble the information. Here we discuss the different methods used to aggregate welfare measures and their applicability to certification schemes involving welfare. Data obtained on a farm can be (i) analysed by an expert who draws an overall conclusion; (ii) compared with minimal requirements set for each measure; (iii) converted into ranks, which are then summed; or (iv) converted into values or scores compounded in a weighted sum (e.g. TGI35L) or using ad hoc rules. Existing methods used at present (at least when used exclusively) may be insufficiently sensitive or not routinely applicable, or may not reflect the multidimensional nature of welfare and the relative importance of various welfare measures. It is concluded that different methods may be used at different stages of the construction of an overall assessment of animal welfare, depending on the constraints imposed on the aggregation process.     

Assessing the density of honey bee colonies at ecosystem scales

1. Information about the density of wild honey bee (Apis spp.) colonies in an ecosystem is central to understanding the functional role of honey bees in that ecosystem, necessary for effective biosecurity response planning, and useful for determining whether pollination services are adequate. However, direct visual surveys of colony locations are not practical at ecosystem scales. Thus, indirect methods based on population genetic analysis of trapped males have been proposed and implemented. 2. In this review, indirect methods of assessment of honey bee colony densities are described, which can be applied at ecosystem scales. The review also describes how to trap males in the field using the Williams drone trap (or virgin queens) the appropriate genetic markers and statistical analyses, and discusses issues surrounding sample size. 3. The review also discusses some outstanding issues concerning the methods and the conversion of estimated colony number to colony density per km². The appropriate conversion factor will require further research to determine the area over which a drone trap draws drones.     

A transformation approach for incorporating monotone or unimodal constraints

Samples of curves are collected in many applications, including studies of reproductive hormone levels in the menstrual cycle. Many approaches have been proposed for correlated functional data of this type, including smoothing spline methods and other flexible parametric modeling strategies. In many cases, the underlying biological processes involved restrict the curve to follow a particular shape. For example, progesterone levels in healthy women increase during the menstrual cycle to a peak achieved at random location with decreases thereafter. Reproductive epidemiologists are interested in studying the distribution of the peak and the trajectory for women in different groups. Motivated by this application, we propose a simple approach for restricting each woman's mean trajectory to follow an umbrella shape. An unconstrained hierarchical Bayesian model is used to characterize the data, and draws from the posterior distribution obtained using a Gibbs sampler are then mapped to the constrained space. Inferences are based on the resulting quasi-posterior distribution for the peak and individual woman trajectories. The methods are applied to a study comparing progesterone trajectories for conception and nonconception cycles.     

From vigilance to violence: Tactics of mate retention in American undergraduates

Although the attraction and selection of mates are central to human reproduction, the retention of acquired mates is often necessary to actualize the promise of reproductive effort. Three empirical studies used act frequency methods to identify, assess the reported performance frequencies of, and evaluate the perceived effectiveness of 19 tactics and 104 acts of human mate guarding and retention. In Study 1 (N = 105), a hierarchical taxonomy of tactics was developed from a pool of nominated acts. We then assessed the reported performance frequencies of 19 retention tactics and 104 acts and tested three hypotheses derived from evolutionary models in an undergraduate sample (N = 102). Study 2 (N = 46) provided an independent test of these hypotheses by assessing the perceived effectiveness of each tactic. Discussion draws implications for sexual poaching, susceptibility to pair-bond defection, and the power of act frequency methods for preserving the proximate specificity and systemic complexity inherent in human mating processes.     

Ethics in Darwin's melancholy vision

Darwinian natural selection draws on Malthus' harsh vision of human society to explain how organisms come to be adapted to their environments. Natural selection produces the appearance of teleology, but requires only efficient causal processes: undirected, heritable variation combined with effects of the variations on survival and reproduction. This paper draws a sharp distinction between the resulting form of backwards-directed teleology and the future-directed teleology we ascribe to intentional human activity. Rather than dismiss teleology as mere illusion, the paper concludes with an account of how future-directed teleology came to be a justifiable part of how we understand ourselves.     

Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models

MOTIVATION: Mapping character state changes over phylogenetic trees is central to the study of evolution. However, current probabilistic methods for generating such mappings are ill-suited to certain types of evolutionary models, in particular, the widely used models of codon substitution. RESULTS: We describe a general method, based on a uniformization technique, which can be utilized to generate realizations of a Markovian substitution process conditional on an alignment of character states and a given tree topology. The method is applicable under a wide range of evolutionary models, and to illustrate its usefulness in practice, we embed it within a data augmentation-based Markov chain Monte Carlo sampler, for approximating posterior distributions under previously proposed codon substitution models. The sampler is found to be more efficient than the conventional pruning-based sampler with the decorrelation times between draws from the posterior reduced by a factor of 20 or more.     

Translational Research and Youth Development

Borrowing the term “translational research” (TR) from medicine, along with some of the ideas and practices that define it, holds promise as a way of linking research more closely to the practice of youth development. However, doing so entails substantial adaptation. TR is more than a new name for applied research. It comprehends the sequence of very different kinds of research that connect new knowledge with practice and ultimately with enhanced youth development. Research syntheses and evidence-based programs and practices are central to TR, which draws on a variety of research methods and traditions, including epidemiology, “basic” research, evaluation, and implementation science. Syntheses are needed in all these areas along with communication among researchers representing them as well as with practitioners. The flow of information is bi-directional; research is informed by practice and practitioners conduct research.     

Psychophysics in functional strength and power training: review and implementation framework

Functional training is considered to be training that attempts to mimic the specific physiological demands of real-life activities. Most approaches to functional training, though, omit important factors that contribute to physiological and neuromotor adaptations. Cognitive factors related to sports influence physiological performance, and subsequently, physiological and neuromotor adaptations. We present a rationale and a theoretical framework by which to create effective functional training methods that incorporate cognitive factors. This framework draws upon recent developments and strong empirical evidence in the areas of dynamic systems theory, perceptual skills training, and motor learning/control. Emphasized within rigorous physical training are practice-related techniques and motor-learning strategies. In particular, mental effort, attention, and intention manipulated in a discovery-learning paradigm provide a framework for functional strength and power training. This framework is suggested to help maximize sport-specific physiological adaptations, and subsequently, sports performance.     

Mind and Spirit: a comparative theory about representation of mind and the experience of spirit

This special issue reports the findings of the Mind and Spirit project. We ask whether different understandings of ‘mind’, broadly construed, might shape the ways that people attend to and interpret thoughts and other mental events – and whether their judgements affect their experience of (what they take to be) gods and spirits. We argue in this collection that there are indeed cultural differences in local theories of minds, in the way social worlds draws the line between interior and exterior, and that these differences do affect the way people sense invisible others. This introduction lays out the ideas that inspired the project and the methods that we used. This is the first report on our work.